In 1989, HCI changed its name to Mercy International-USA (MI) and established its new headquarters in Michigan. The organization also maintained branch offices in such far-flung locations as Albania, Bosnia, Canada, Kenya, Pakistan, the Philippines, and Switzerland. Some of these regional chapters had names that differed slightly from one another; e.g., the Canadian branch was known as the Mercy International Relief Agency. Regardless of name or location, however, MI's official mission was to deliver emergency humanitarian aid—food, medicine, clothing, and shelter to people in need—“especially in the cases of natural catastrophe and war.” MI also helped to develop hospitals and orphanages in Albania, and was known as well for its charitable activities on behalf of Bosnian Muslims.

In MI's earliest days (prior to the name change), its Pakistan chapter was headed by Ahmed Khadr, a close associate of Osama bin Laden. Khadr was succeeded in this post in 1988 by Zahid Shaikh Mohammed (ZSM), the brother of 9/11 mastermind Khalid Shaikh Mohammed and the uncle of Ramzi Yousef (a key planner of the 1993 World Trade Center bombing). In the spring of 1993, U.S. investigators, while while searching for Yousef, raided ZSM's home and found numerous documents and photographs indicating close links and even a friendship between ZSM and Osama bin Laden. Eventually the Kuwaiti government confirmed that ZSM was in fact a member of al Qaeda.

ZSM retained his post with MI until about February 1995, when Ramzi Yousef was arrested in Pakistan. At that point, investigators learned that Yousef, who had ZSM's telephone number listed in his private directory, had been conducting phone correspondence with MI's Pakistan office. Pakistani investigators promptly raided MI's local headquarters but failed to apprehend ZSM, who had already fled.

By late 1996, U.S. intelligence officials began monitoring telephone calls to and from MI's Kenyan branch, on suspicion of the organization's possible involvement in terrorist plots and activities. Shortly before the infamous al Qaeda bombings of two American embassies in Kenya and Tanzania in August 1998, MI director Ahmad Sheik Adam and al Qaeda leader Osama bin Laden corresponded by phone on numerous occasions. Soon after the bombings, local anti-terrorism agents raided raided MI's Kenya office and discovered incriminating files belonging to Wadih El-Hage, an al Qaeda operative living in Nairobi. Those files indicated that MI had issued identity cards for bin Laden and fellow al Qaeda leaders Ali Mohamed and Mohammed Atef.

Al-Qaeda operative L'Houssaine Khertchou later testified, during his 2001 trial, that his organization was interacting on a regular basis with MI's Kenya branch, which employed a number of al Qaeda operatives. Khertchou further revealed that MI—in collaboration with the International Islamic Relief Organization—had helped bankroll the 1998 embassy bombings.

As of 1999, Khaldoun Dia Eddine, manager of MI's Albania chapter, also served as head of the Gulf Office—an Al Taqwa Bank subsidiary that the Italian government had investigated five years earlier for its ties to an Algerian militant group affiliated with al Qaeda. (Al Taqwa Bank was founded by the Muslim Brotherhood.) In addition, Eddine managed a major weapons-delivery channel for the Kosovo Liberation Army, a venture in which he received financial and logistic support from the Muslim World League.

In 1999 as well, U.S. investigators uncovered a financial link between MI and Baitul Mal Inc. (BMI), a New Jersey-based investment firm with connections to many suspected terrorist financiers—including some affiliated with Hamas and al Qaeda. It was also believed that BMI had been involved in financing the 1998 embassy bombings in East Africa.

In addition to the individuals named above, MI's most noteworthy officials and allies included the following:

Kuwaiti Muslim Brotherhood chief Jassem Muhallal el-Yassin, who served as an MI chairman and collaborated closely with Sudanese leader Hassan el-Tourabi to coordinate support for Islamist movements in Maghreb